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Due to legal restrictions imposed by the Yugoslavian government during the 1980s, the first aircraft was flown secretly in the evening, between dusk and dark. The flying times and triangular shape of the hang-glider style wings earned the aircraft the nickname "bats" which was adopted by the company naming themselves after the Latin word for bat, pipistrellus.[2]

In August 2012, Pipistrel was hit by a brief week-long import ban issued by the Federal Aviation Administration. Pipistrel had opened a factory in Italy to benefit from the country's bilateral agreements with the United States. During a routine check, the FAA was unable to locate Pipistrel's Italian factory on Google Earth and banned the import of some of Pipistrel's products.[4]

In July 2015, Siemens, provider of the Dynadyn 60-kilowatt motor used in the Alpha Electro trainer, warned Pipistrel that it should not use its motors for overwater flights, just as Pipistrel was about to launch a historic electric-powered flight across the English Channel and back. As it turns out, Airbus was preparing exactly the same Louis Blériot-like exploit, with a plane powered by a motor also provided by Siemens, and it was speculated that Siemens was pressured by Airbus.[5][6]

In February 2016, Pipistrel ran the most powerful hybrid electric powertrain in aviation to date, as a part of the project HYPSTAIR.[9][10]

On 29 September 2016 the world’s first four-seat passenger aircraft powered by a zero-emission hydrogen fuel cell propulsion system accomplished a successful first public flight. Pipistrel was one of the partners in the "HY4" project.[11][12]

In December 2007, the aircraft Taurus electro took off as the world’s first fully electric 2-seat aircraft. It was named as one of the most important innovations in 2008 by the American magazine Popular Science. In 2010, it won a gold medal at the Biennial of Industrial Design.